Yep, its Apple magic! ;-}
Sadly, there is some logic within the power adapter that interacts with the system via the middle connector. The connector it's self is not the issue it's the signal within the middle pin between the power adapter and the system thats is the issue here.
Basically, you'll need to get a real power adapter unit to run or charge your systems battery. Hopefully you didn't damage the logic inside your system with your home made power source.